Feedback from both Rachel and Gos that we need to ensure people understand what calculations are going on in the background.

Maybe link somewhere to our docs for the curious:
http://intermine.readthedocs.io/en/latest/embedding/list-widgets/enrichment-widgets/

There used to be A-Z / Z-A sort but this stopped working at some point, and we should probably allow other sort types too, like most recent, by type, etc.

From feedback via Gos:

Mouse-over p-value explanation good but text needs to be more informative i.e. needs more
explanation of what has actually been done. Or maybe the "Enrichment" header needs a "?".
Filter enrichment box: works, really nice! Works on internal substrings - like!

Nice that contrasting grey for miRNNA enrichment when (0)
Maybe, shock, we shouldn't call enrichment "enrichment" but "unexpectedly common" or
something like that. Or use that for the top title or top title explanation and then use
enrichment below as more concise.

this is the report page for flymine / adh. Empty rows?!

Items which should have no content when mines are switched (but currently do)

• Region Search
• Template Filters
• Upload
• Search

Most of these items make no sense when in the context of a different Mine

Discovered by @julie-sullivan's eagle eyes. To reproduce:

Run template Protein Domain --> Protein + Genes
Column to enrich is protein. switch to gene. the protein widgets stay but lose their headings.

Visual example - the widgets with missing headers shouldn't be present on the page at all.

For example, one might reasonably expect the search phrase "organism region" to return a response for the template "Organism --> All intergenic regions".

This is probably a thing in most of the other inline filter / search boxes too so probably would benefit from some common functionality.

Make configurable to be either imtables or light tables depending on user preference. We've had strong feelings on both sides

examples:

currently if you switch mines in the dev section, you'll have all the old lists as well as the new mine's lists.

When a list operation is performed the list is auto-named and added almost silently to the list of lists. We need to be able to name lists and:

a) give feedback it's been added (toast? animation? other?)
b) give feedback if it isn't added for any reason...

jsp default behaviour is to require input before proceeding according to @julie-sullivan (correct me if wrong).

we currently add the first one, whatever it is, in redgenes. should match 1.x behaviour? also, make sure that dropdown arrow is readable. it's become truncated and confusing.

When you click the star, it just selects or deselects the row.

This is probably my fault; I suspect we need to stop the clicklistener that selects and deselects the whole row from taking control of the star click.

Report pages for types that have spaces in them don't work properly.

examples:

http://devredgenes.apps.intermine.org/#/reportpage/flymine-beta/miRNA Target/90070104
http://devredgenes.apps.intermine.org/#/reportpage/flymine-beta/Intergenic Region/103079005

results in

rather than a report page. This may drill down to imcljs but I"m unsure at this point

There's a "show more" button, maybe we should have a "show fewer" button as well?

example is humanmine/bmp4

the report page assumes that the gene you're looking at is for the mine's default organism. if a mine contains more than one organism, all non-default organism genes will have problems. need to get the organism in the query from the report page's summary fields (?) instead.

Right now whatever we input into the box is submitted to the sever. When the input is invalid we don't get verbose or meaningful error messages back, so we should validate the regions clientside before submission.

Demonstrative example:

The 'ss' appended to the end of the input in that screenshot results in a 500 from the server, and no results for any of the regions.

Add chromosome location and the FASTA sequence to the top of the page. suggested by rachel.

for example, we might expect to see equals in the dropdown list:

Possible place to start looking: https://github.com/intermine/redgenes/blob/dev/src/cljs/redgenes/components/ui/constraint.cljs#L7

example:

To reproduce in beta flymine: use Gene --> Regulatory elements template.

Probably an easy fix if we set the max width to 98vw and handle wide-table overflow.

visual example:

the reason this happens is the container holding the table has overflow set to scrolling or hidden

Other times it appears but has wrong results. Possibly tied to #19?

Template search should be the first thing in the trail, not the results.

Screenshot of the functionality in the jsp UI:

Is this information available via a webservice do we know? @joshkh @julie-sullivan

It would be nice if the filters and search box were fixed to the top of the page.

Because we might want proteins or lists of other things.

'nuff said really. See also #43

We have feedback, but it could be even more explicit. Gos suggested mentioning the name of the current category to reinforce things - "No templates available in the expression category. Try searching all categories"

If the only ids in the id resolver are bad IDs, there isn't going to be anything in the results table....

as you can see in this image, there are no enrichment widgets available for the types displayed in the current results page, but the top left bit likes to pretend its enriching genes anyway. Wrong! Sad.

This is an often-requested feature that gos likes.

Search across templates, filter by type, etc.

When I fixed the back button I killed deep linking to a page. http://localhost:3449/#/upload should take me to the upload page but it just lands me on the homepage.

Internal links work, it's just the initial route dispatch on pageload that is broken.

Right now (I believe) the combine, difference, and intersect buttons expect exactly two lists and will cause odd behaviour if there are more than two selected. We need to either:

a) prevent operations on more than two lists
b) make it so that these operations work as expected.

I suspect a) will be much easier and is probably the saner short term solution.

Right now when we deploy a new script version, the version number is appended to the URL to cache-bust the app.js file - but localstorage isn't expired when this happens and probably should be.

never shows results even though same code works fine on a local dev machine!!

example - there is a search term in the search box, no results shown:

If we cache authentication tokens (which we do) and we get a 401 for an anonymous token - I think this happens when a token expires due to a rebuild or a certain timeout, we need to automatically delete the token and try again. Or maybe @joshkh had some session ideas about how to handle this?

see the screenshot: lat two items are both zen, both contribute to the count, but ultimately only one will be in the resulting list.

The upload screen text suggests multiple items can be removed but the functionality to allow a user to select multiple ids died at some point. Marking as enhancement rather than bug because everything works just fine without this feature and there are no obvious errors.

each item should have a count of the number of items enriched with that term

Short term let's hide the button?

in the results page, you are able to navigate through history and "drill down" into enrichment table. If you click on an enrichment type, the table will update to show you a table of enriched results. The enrichment continues to show on the left but doesn't change its results to reflect the new enriched elements in the table - it's still enriching on the original set of results at the start of the history.

Quick notes: the fetch ids method may need to be updated, or something that feeds in to this method, as it doesn't seem to be updating its query in response to the new results shown in the imtable. perhaps it needs to look into the history? the tables and enrichment don't appear to be the cause.

The template count (big blue button in screenshow) shows "view N rows", but the count doesn't reset in between switching templates and takes a second or two to update.

This means that sometimes it tells complete lies! This screenshot says "view 7810 rows", but for a second or two it said "view 1 row", because the previous template I'd been viewing had only one result. It'd be better to remove or disable this button until we have an explicit up to date count. I also suspect the state of the template may be incorrect for the preview table.

Add quick links / data tabs to the top of the report page to help navigate long pages and give the user an idea of what data's available without having to scroll through it all. (Suggested by rachel)